This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We are developing a method for the multiresolution comparison of biomolecular electrostatic potentials without the need for global structural alignment of the biomolecules. The underlying computational geometry algorithm uses multiresolution attributed contour trees (MACTs) to compare the topological features of volumetric scalar fields. We apply the MACTs to compute electrostatic similarity metrics for a large set of protein chains with varying degrees of sequence, structure, and function similarity. For calibration, we also compute similarity metrics for these chains by a more traditional approach based upon 3D structural alignment and analysis of Carbo similarity indices. Moreover, because the MACT approach does not rely upon pairwise structural alignment, its accuracy and efficiency promise to perform well on future large-scale classification efforts across groups of structurally diverse proteins. The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method;i.e., it is able to accurately cluster proteins into functionally relevant groups which demonstrate strong dependence on ligand binding sites.